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Find video protocols related to scientific articles indexed in Pubmed.
High-Resolution Mass Spectrometry Associated with Data Mining Tools for the Detection of Pollutants and Chemical Characterization of Honey Samples.
J. Agric. Food Chem.
PUBLISHED: 11-11-2014
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Analytical methods for food control are mainly focused on restricted lists of well-known contaminants. This paper shows that liquid chromatography-high-resolution mass spectrometry (LC/ESI-HRMS) associated with the data mining tools developed for metabolomics can address this issue by enabling (i) targeted analyses of pollutants, (ii) detection of untargeted and unknown xenobiotics, and (iii) detection of metabolites useful for the characterization of food matrices. A proof-of-concept study was performed on 76 honey samples. Targeted analysis indicated that 35 of 83 targeted molecules were detected in the 76 honey samples at concentrations below regulatory limits. Furthermore, untargeted metabolomic-like analyses highlighted 12 chlorinated xenobiotics, 1 of which was detected in lavender honey samples and identified as 2,6-dichlorobenzamide, a metabolite of dichlobenil, a pesticide banned in France since 2010. Lastly, multivariate statistical analyses discriminated honey samples according to their floral origin, and six discriminating metabolites were characterized thanks to the MS/MS experiments.
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Annotation of the human serum metabolome by coupling three liquid chromatography methods to high-resolution mass spectrometry.
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
PUBLISHED: 04-11-2014
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This work aims at evaluating the relevance and versatility of liquid chromatography coupled to high resolution mass spectrometry (LC/HRMS) for performing a qualitative and comprehensive study of the human serum metabolome. To this end, three different chromatographic systems based on a reversed phase (RP), hydrophilic interaction chromatography (HILIC) and a pentafluorophenylpropyl (PFPP) stationary phase were used, with detection in both positive and negative electrospray modes. LC/HRMS platforms were first assessed for their ability to detect, retain and separate 657 metabolite standards representative of the chemical families occurring in biological fluids. More than 75% were efficiently retained in either one LC-condition and less than 5% were exclusively retained by the RP column. These three LC/HRMS systems were then evaluated for their coverage of serum metabolome. The combination of RP, HILIC and PFPP based LC/HRMS methods resulted in the annotation of about 1328 features in the negative ionization mode, and 1358 in the positive ionization mode on the basis of their accurate mass and precise retention time in at least one chromatographic condition. Less than 12% of these annotations were shared by the three LC systems, which highlights their complementarity. HILIC column ensured the greatest metabolome coverage in the negative ionization mode, whereas PFPP column was the most effective in the positive ionization mode. Altogether, 192 annotations were confirmed using our spectral database and 74 others by performing MS/MS experiments. This resulted in the formal or putative identification of 266 metabolites, among which 59 are reported for the first time in human serum.
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Evaluation of horse urine sample preparation methods for metabolomics using LC coupled to HRMS.
Bioanalysis
PUBLISHED: 04-08-2014
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Horse urine is the medium of choice for the implementation of metabolomic approaches aimed at improving horse doping control. However, drug analysis in this biofluid is a challenging task due to the presence of large amounts of interfering compounds. METHODOLOGY & RESULTS: A comparative study of sample preparation has been conducted to evaluate five sample-preparation methods, namely acetonitrile precipitation, proteinase K hydrolysis, membrane filtration and sample dilution with water by factors of five and 20, for metabolome analysis using liquid chromatography coupled to high resolution mass spectrometry. Assessment was performed at both global and targeted levels, by using a few thousand features obtained from peak detection software, and internal standards and 100 annotated or identified metabolites.
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A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.
Rapid Commun. Mass Spectrom.
PUBLISHED: 04-01-2014
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High-energy collision-induced dissociation (CID) spectra of isomeric RNA/DNA chimeras using matrix-assisted laser desorption/ionization time-of-flight LIFT mass spectrometry (MALDI-LIFT-TOF/TOF) can potentially be applied for an exhaustive fragment characterization in a nucleic acid sequencing scheme. These chimeras contain deoxynucleotides and at the 3'-end a ribonucleotide with a 3'-phosphate group.
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Comparison of the activation time effects and the internal energy distributions for the CID, PQD and HCD excitation modes.
J Mass Spectrom
PUBLISHED: 03-12-2014
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Reproducibility among different types of excitation modes is a major bottleneck in the field of tandem mass spectrometry library development in metabolomics. In this study, we specifically evaluated the influence of collision voltage and activation time parameters on tandem mass spectrometry spectra for various excitation modes [collision-induced dissociation (CID), pulsed Q dissociation (PQD) and higher-energy collision dissociation (HCD)] of Orbitrap-based instruments. For this purpose, internal energy deposition was probed using an approach based on Rice-Rampserger-Kassel-Marcus modeling with three thermometer compounds of different degree of freedom (69, 228 and 420) and a thermal model. This model treats consecutively the activation and decomposition steps, and the survival precursor ion populations are characterized by truncated Maxwell-Boltzmann internal energy distributions. This study demonstrates that the activation time has a significant impact on MS/MS spectra using the CID and PQD modes. The proposed model seems suitable to describe the multiple collision regime in the PQD and HCD modes. Linear relationships between mean internal energy and collision voltage are shown for the latter modes and the three thermometer molecules. These results suggest that a calibration based on the collision voltage should provide reproducible for PQD, HCD to be compared with CID in tandem in space instruments. However, an important signal loss is observed in PQD excitation mode whatever the mass of the studied compounds, which may affect not only parent ions but also fragment ions depending on the fragmentation parameters. A calibration approach for the CID mode based on the variation of activation time parameter is more appropriate than one based on collision voltage. In fact, the activation time parameter in CID induces a modification of the collisional regime and thus helps control the orientation of the fragmentation pathways (competitive or consecutive dissociations).
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Evidence for ion-ion interactions between peptides and anions (HSO?? or ClO??) derived from high-acidity acids.
J Mass Spectrom
PUBLISHED: 03-08-2014
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The existence of gas-phase electrostatic ion-ion interactions between protonated sites on peptides ([Glu] Fibrinopeptide B, Angiotensin I and [Asn(1), Val(5)]-Angiotensin II) and attaching anions (ClO4(-) and HSO4(-)) derived from strong inorganic acids has been confirmed by CID MS/MS. Evidence for ion-ion interactions comes especially from the product ions formed during the first dissociation step, where, in addition to the expected loss of the anion or neutral acid, other product ions are also observed that require covalent bond cleavage (i.e. H2O loss when several carboxylate groups are present, or NH3 loss when only one carboxylate group is present). For [[Glu] Fibrinopeptide B?+?HSO4](-), under CID, H2O water loss was found to require less energy than H2SO4 departure. This indicates that the interaction between HSO4(-) and the peptide is stronger than the covalent bond holding the hydroxyl group, and must be an ion-ion interaction. The strength and stability of this type of ion-pairing interaction are highly dependent on the accessibility of additional mobile charges to the site. Positive mobile charges such as protons from the peptide can be transferred to the attaching anion to possibly form a neutral that may depart from the complex. Alternatively, an ion-ion interaction can be disrupted by a competing proximal additional negatively charged site of the peptide that can potentially form a salt bridge with the positively charged site and thereby facilitate the attaching anion's departure.
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Bacterial detection using unlabeled phage amplification and mass spectrometry through structural and nonstructural phage markers.
J. Proteome Res.
PUBLISHED: 02-19-2014
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According to the World Health Organization, food safety is an essential public health priority. In this context, we report a relevant proof of feasibility for the indirect specific detection of bacteria in food samples using unlabeled phage amplification coupled to ESI mass spectrometry analysis and illustrated with the model phage systems T4 and SPP1. High-resolving power mass spectrometry analysis (including bottom-up and top-down protein analysis) was used for the discovery of specific markers of phage infection. Structural components of the viral particle and nonstructural proteins encoded by the phage genome were identified. Then, targeted detection of these markers was performed on a triple quadrupole mass spectrometer operating in the selected reaction monitoring mode. E. coli at 1 × 10(5), 5 × 10(5), and 1 × 10(6) CFU/mL concentrations was successfully detected after only a 2 h infection time by monitoring phage T4 structural markers in Luria-Bertani broth, orange juice, and French bean stew ("cassoulet") matrices. Reproducible detection of nonstructural markers was also demonstrated, particularly when a high titer of input phages was required to achieve successful amplification. This strategy provides a highly time-effective and sensitive assay for bacterial detection.
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Structural studies of the sBBI/trypsin non-covalent complex using covalent modification and mass spectrometry.
Rapid Commun. Mass Spectrom.
PUBLISHED: 02-06-2014
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The study of protein recognition sites is crucial for understanding the mechanisms of protein interaction. Mass spectrometry can be a method of choice for the investigation of the contact surface within the protein non-covalent complexes.
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The Pauson-Khand mechanism revisited: origin of CO in the final product.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 01-21-2014
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The mechanism of the Pauson-Khand reaction has been studied by mass spectrometry and it has been found, through ion-molecule reaction with (13) CO, that the carbon monoxide incorporated into the product cyclopentenone is one that has been retained within the complex. Theoretical and kinetic calculations support this finding, which provides a complementary explanation for the effect of Pauson-Khand promoters.
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Charge Enhancement of Single-Stranded DNA in Negative Electrospray Ionization Using the Supercharging Reagent Meta-nitrobenzyl Alcohol.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 08-07-2013
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Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (Itot), increase the highest observed charge states (zhigh), and raise the average charge states (zavg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER1%) and charge enhancement coefficients (CEC1%) were introduced. The SER1%, (defined as the quotient of total oligonucleotide ion abundances with 1 % m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC1% values (defined as the average charge state in the presence of 1 % m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.
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Greater prognostic value of peak VO2 after exercise training program completion in heart failure patients.
Int. J. Cardiol.
PUBLISHED: 07-08-2013
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Exercise capacity, best reflected by peak exercise oxygen consumption (peak VO(2)), is a powerful prognostic factor in patients with chronic heart failure (CHF). However, the optimal time to assess exercise capacity for prognosis remains unclear and whether an exercise training program (ETP) to improve exercise capacity alters the prognostic value of cardiopulmonary exercise (CPX) testing variables in CHF is unknown.
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High-resolution mass spectrometry and partial de novo sequencing constitute a useful approach for determining the profile of chemokine secretion following the stimulation of human intestinal epithelial cells.
Rapid Commun. Mass Spectrom.
PUBLISHED: 06-29-2013
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Intestinal epithelial cells (IEC) secrete many chemokines in response to proinflammatory stimuli. We investigated their role in the mucosal inflammatory response in the intestine, by developing a non-targeted approach for analyzing the profile of peptides secreted by stimulated IEC, based on differential mass spectrometry analysis.
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MALDI/Post Ionization-Ion Mobility Mass Spectrometry of Noncovalent Complexes of Dopamine Receptors Epitopes.
J. Proteome Res.
PUBLISHED: 03-25-2013
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Protein domains involved in receptor heteromer formation are disordered and rich in the amino acids necessary for the formation of noncovalent complexes (NCX). We present mass spectral NCX data from proteins and protein receptors epitopes obtained by combining ion mobility (IM) and MALDI. We focus on NCX involved in heteromer formation occurring between epitopes of the Dopamine D2 (D2R) and Adenosine A2A receptors (A2AR) as well as D2R and the ?2 nicotinic (NR) receptors subunit. The IM data yield information on the gas phase conformation of the singly charged NCX which are observed either directly from MALDI or as codesorbed neutrals that are subsequently postionized by a time-delayed excimer laser pulse directed onto a portion of the neutral plume created by the MALDI desorption laser. Imaging mass spectrometry of the matrix/epitope dried droplet surface shows that the acidic and basic epitopes and their NCX are found to be spatially collocated within regions as small as 25 × 50 ?m(2). Subtle differences in the relative abundance of protonated and cationized NCX and epitopes are measured in spatial regions near the sodium-rich outer border of the droplet.
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ESI formation of a Meisenheimer complex from tetryl and its unusual dissociation.
J Mass Spectrom
PUBLISHED: 03-16-2013
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The reactivity of the explosive tetryl (N-methyl-N,2,4,6-tetranitroaniline; Mw = 287 u) was studied using electrospray ionization in negative mode. The main species detected in the spectrum corresponds to the ion observed at m/z 318 (previously assumed to be the odd-electron ion [tetryl + HNO](-•), C7H6O9N6). In this study, we show using D-labeling combined with high-resolution mass spectrometry that this species corresponds to an even-electron anion (i.e. C8H8O9N5), resulting from the formation of a Meisenheimer complex between tetryl and the methanol used as the solvent. Fragmentation of this complex under CID conditions revealed an unexpected fragment: the formation of a 2,4,6-trinitrophenoxide anion at m/z 228. (18)O-labeling combined with quantum chemical calculations helped us better understand the reaction pathways and mechanisms involved in the formation of this product ion. This occurs via a transition state leading to a SN2-type reaction, consequently evolving toward an ion-dipole complex. The latter finally dissociates into deprotonated picric acid.
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Critical evaluation of kinetic method measurements: possible origins of nonlinear effects.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 02-07-2013
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The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities (?H° acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.
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Collision cell pressure effect on CID spectra pattern using triple quadrupole instruments: a RRKM modeling.
J Mass Spectrom
PUBLISHED: 02-05-2013
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Control of the ion internal energy in mass spectrometry is needed to establish a workable mass spectral library. The purpose of this study is to understand and to compare the pressure effects on the collision-induced dissociation (CID) spectrum pattern recorded using triple quadrupole instruments. The monoprotonated Leucine enkephalin [YGGFL, H(+)] was used as a thermometer molecule to calibrate the electrospray ionization (ESI) and the CID internal energies deposited on the molecular species and the time scale of ion decompositions. The survival yield and the ratio of a(4)/b(4) fragment ions were mainly monitored. The energy uptake for the ESI source geometry used in our study has no impact on the CID spectrum fingerprint. The collision cell pressure for the [YGGFL, H(+)] has a major influence on the SY curves slope and on the experimental time scale. To demonstrate the pressure effect on internal energy distribution, three models (threshold, thermal and collisional) based on RRKM theory were built using the Masskinetics software. As a result, the limit of each model is discussed, and the investigation demonstrates that the thermal model, using truncated Maxwell-Boltzmann internal energy distribution, is well-suited for simulating the experimental data at high pressure widely used in the analytical conditions.
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Characterization of an electron ionization source trap operating in the presence of a magnetic field through computer simulation.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 01-25-2013
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We explore the feasibility of conducting electron ionization (EI) in a radio-frequency (rf) ion source trap for mass spectrometry applications. Electrons are radially injected into a compact linear ion trap in the presence of a magnetic field used essentially to lengthen the path of the electrons in the trap. The device can either be used as a stand-alone mass spectrometer or can be coupled to a mass analyzer. The applied parallel magnetic field and the oscillating rf electric field produced by the trap give rise to a set of coupled Mathieu equations of motion. Via numerical simulations, electron trajectories are studied under varying intensities of the magnetic field in order to determine the conditions that enhance ion production. Likewise, the dynamic behavior of the ions are investigated in the proposed EI source trap and the fast Fourier transform FFT formalism is used to obtain the frequency spectrum from the numerical simulations to study the motional frequencies of the ions which include combinations of the low-frequency secular and the high-frequency micromotion with magnetron and cyclotron frequencies. The dependence of these motional frequencies on the trapping conditions is examined and particularly, the limits of applying a radial magnetic field to the EI ion trap are characterized.
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Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry.
J Mass Spectrom
PUBLISHED: 01-24-2013
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Organophosphorus compounds have played important roles as pesticides, chemical warfare agents and extractors of radioactive material. Structural elucidation of phosphonates poses a particular challenge because their initial forms can be hydrolyzed, thus, degradation products may predominate in samples acquired in the field. The analysis of non-volatile organophosphorus compounds and their degradation products is possible using electrospray tandem mass spectrometry ESI-MS/MS. Here, we present a generic strategy that allows the unambiguous identification of substituents for two families of organophosphorus compounds: the phosphonates and phosphates. General fragmentation rules were deduced based on the study of decomposition pathways of 55 organophosphorus esters, including examples found in the literature. Multistage MS (MS(n)) experiments at high resolution in a hybrid mass spectrometer provide accurate mass measurements, whereas collision-induced dissociation experiments in a triple quadrupole give access to small fragment ions. The creation of a specific nomenclature for each possible structure of organophosphorus compound, depending on the alkyl side chain linked to the oxygen, was achieved by applying these fragmentation rules. This led to the creation of an identification tree based upon the unique consecutive decomposition pathways uncovered for each individual compound. Hence, seven structural motifs were created that orient an unequivocal identification using the identification tree. Despite the similar structures of the ensemble of phosphate and phosphonate esters, distinct identifications based upon characteristic neutral losses and diagnostic fragment ions were possible in all cases.
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Instrumental dependent dissociations of n-propyl/isopropyl phosphonate isomers: evaluation of resonant and non-resonant vibrational activations.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 01-09-2013
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Structural elucidation and distinction of isomeric neurotoxic agents remain a challenge. Tandem mass spectrometry can be used for this purpose in particular if a "diagnostic" product ion is observed. Different vibrational activation methods were investigated to enhance formation of diagnostic ions through consecutive processes from O,O-dialkyl alkylphosphonates. Resonant and non-resonant collisional activation and infrared multiphoton dissociation (IRMPD) were used with different mass spectrometers: a hybrid quadrupole Fourier transform ion cyclotron resonance (Qh-FTICR) and a hybrid linear ion trap-Orbitrap (LTQ/Orbitrap). Double resonance (DR) experiments, in ion cyclotron resonance (ICR) cell, were used for unambiguous determination of direct intermediate yielding diagnostic ions. From protonated n-propyl and isopropyl O-O-dialkyl-phosphonates, a diagnostic m/z 83 ion characterizes the isopropyl isomer. This ion is produced through consecutive dissociation processes. Conditions to favor its formation and observation using different activation methods were investigated. It was shown that with the LTQ, consecutive experimental steps of isolation/activation with modified trapping conditions limiting the low mass cut off (LMCO) effect were required, whereas with FT-ICR by CID and IRMPD the diagnostic ion detection was provided only by one activation step. Among the different investigated activation methods it was shown that by using low-pressure conditions or using non-resonant methods, efficient and fast differentiation of isomeric neurotoxic agents was obtained. This work constitutes a unique comparison of different activation modes for distinction of isomers showing the instrumental dependence characteristic of the consecutive processes. New insights in the dissociation pathways were obtained based on double-resonance IRMPD experiments using a FT-ICR instrument with limitation at low mass values.
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Prevalence of K-RAS Codons 12 and 13 Mutations in Locally Advanced Head and Neck Squamous Cell Carcinoma and Impact on Clinical Outcomes.
Int J Otolaryngol
PUBLISHED: 01-04-2013
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Background. RAS gene mutations have an impact on treatment response and overall prognosis for certain types of cancer. Objectives. To determine the prevalence and impact of K-RAS codons 12 and 13 mutations in patients with locally advanced HNSCC treated with primary or adjuvant chemo-radiation. Methods. 428 consecutive patients were treated with chemo-radiation therapy and followed for a median of 37 months. From these, 199 paraffin embedded biopsy or surgical specimens were retrieved. DNA was isolated and analyzed for K-RAS mutational status. Results. DNA extraction was successful in 197 samples. Of the 197 specimens, 3.5% presented K-RAS codon 12 mutations. For mutated cases and non-mutated cases, complete initial response to chemoradiation therapy was 71 and 73% (P = 0.32). LRC was respectively 32 and 83% (P = 0.03), DFS was 27 and 68% (P = 0.12), distant metastasis-free survival was 100 and 81% (P = 0.30) and OS was 57 and 65% (P = 0.14) at three years. K-Ras codon 13 analysis revealed no mutation. Conclusion. K-RAS codon 12 mutational status, although not associated with a difference in response rate, may influence the failure pattern and the type of therapy offered to patients with HNSCC. Our study did not reveal any mutation of K-RAS codon 13.
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Identification and characterization of apelin peptides in bovine colostrum and milk by liquid chromatography-mass spectrometry.
J. Proteome Res.
PUBLISHED: 10-13-2011
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Apelin peptides were recently identified as endogenous ligands of the APJ receptor. It has been hypothesized that these peptides are initially provided to the newborn by nursing and might be involved in gastrointestinal tract development. As apelin peptides may have different effects on the APJ receptor as a function of their size, knowledge of their exact structure in early milk is essential to clarify their action in gastrointestinal tract development. Bovine colostrum is thought to contain high concentrations of a wide diversity of apelin peptides, but none of them have yet been rigorously characterized. To identify and monitor apelin peptides in bovine colostrum, we developed a cation exchange extraction step followed by untargeted liquid chromatography coupled to high resolution and high mass accuracy mass spectrometry (LTQ-Orbitrap). Using this approach, we characterized 46 endogenous apelin peptides in bovine colostrum, which varied in relative abundance from one colostrum to another. Mature as well as commercial milk samples were also studied. Taken together, our data demonstrate that the multiplicity and variability of apelin peptides are biologically relevant and change during milk maturation to reach a more constant composition in mature milk.
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Heparin-like glycosaminoglycan/amine salt-bridge interactions: a new potential tool for HLGAGs analysis using mass spectrometry.
J Mass Spectrom
PUBLISHED: 07-12-2011
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Characterization of glycosaminoglycans poses a challenge for current analytical techniques, as they are highly acidic, polydisperse and heterogeneous compounds. The purpose of this study is the separation and analysis of a partially depolymerized heparin-like glycosaminoglycan by on-line ion-pairing reversed-phase high-performance liquid chromatography/electrospray mass spectrometry. The gas-phase behavior of two synthesized glycosaminoglycans has been investigated. Dibutylamine was found to be the best suited ion-pairing reagents for mass spectrometry analysis. The optimized ion-pairing conditions provide reproducible and easily interpretable electrospray mass spectra in both negative and positive ESI modes. The glycosaminoglycans are detected as a non-covalent complex with amines. In fact, the observed ionic species and their gas-phase dissociation under CID conditions revealed the presence of salt bridge interactions in the gas phase.
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Possible conformational change within the desolvated and cationized sBBI/trypsin non-covalent complex during the collision-induced dissociation process.
Rapid Commun. Mass Spectrom.
PUBLISHED: 05-21-2011
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Electrospray ionization mass spectrometry (ESI-MS) has become an analytical technique widely used for the investigation of non-covalent protein-protein and protein-ligand complexes due to the soft desolvation conditions that preserve the stoichiometry of the interacting partners. Dissociation studies of solvated or desolvated complexes (in the source and in the collision cell, respectively) allow access to information on protein conformation and localization of the metal ions involved in protein structure stabilization and biological activity. The complex of bovine trypsin and small soybean Bowman-Birk inhibitor (sBBI) was studied by ESI-MS to determine changes occurring within the complex during its transfer from droplets to the gas phase independently of the ion polarity. Under collision-induced dissociation (CID) conditions, unexpected binding of the Ca(2+) ion (cofactor of native trypsin) to the inhibitor molecule was observed within the desolvated sBBI/trypsin/Ca(2+) complex (with a 1:1:1 stoichiometry). This formal gas-phase migration of the calcium ion from trypsin to the inhibitor may be related to conformational rearrangements in the solvent-free and likely collapsed complex. However, under conditions leading to the increase in complex charge state, the appearance of the cationized trypsin molecule was detected during complex dissociation, thus reflecting different pathways of the evolution of complex conformation.
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Hyalinizing clear cell carcinoma: a case report and review of the literature.
Oral Surg Oral Med Oral Pathol Oral Radiol Endod
PUBLISHED: 02-22-2011
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Hyalinizing clear cell carcinoma (HCCC) is a low-grade malignancy with infiltrative growth pattern. It affects mainly the minor salivary glands of adult women. The most frequent locations of this tumor are the palate and tongue. HCCC shows a poorly circumscribed, infiltrative, and essentially monomorphic population of clear cells with few mitoses and almost no nuclear or cellular pleomorphism. These cells form trabeculae, cords, islands, and/or nests, circumscribed by variable amounts of hyalinized fibrous bands with foci of myxohyaline stroma. S-100 protein, muscle-specific actin, smooth muscle actin, myosin, and calponin are consistently negative, which strongly indicates the absence of myoepithelial cell differentiation in this tumor. We present a case of HCCC affecting the upper vestibule in a 53-year-old man. The patient was treated by surgery and postoperative radiation and did not show recurrence or distant metastases 3 years after treatment. Discussed also are the clinical and pathologic features of this tumor along with the differential diagnosis and a literature review.
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Topoisomer differentiation of molecular knots by FTICR MS: lessons from class II lasso peptides.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 02-10-2011
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Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminal macrolactam ring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collision-induced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECD spectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c•/z from c/z•) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions (b/•(n)). We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z• and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture.
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Simultaneous quantification and qualification of synacthen in plasma.
Anal Bioanal Chem
PUBLISHED: 09-02-2010
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Tetracosactide (Synacthen), a synthetic analogue of adrenocorticotropic hormone (ACTH), can be used as a doping agent to increase the secretion of glucocorticoids by adrenal glands. The only published method for anti-doping control of this drug in plasma relies on purification by immunoaffinity chromatography and LC/MS/MS analysis. Its limit of detection is 300 pg/mL, which corresponds to the peak value observed 12 h after 1 mg Synacthen IM administration. We report here a more sensitive method based on preparation of plasma by cation exchange chromatography and solid-phase extraction and analysis by LC/MS/MS with positive-mode electrospray ionization using 7-38 ACTH as internal standard. Identification of Synacthen was performed using two product ions, m/z 671.5 and m/z 223.0, from the parent [M?+?5H](5+) ion, m/z 587.4. The recovery was estimated at 70%. A linear calibration curve was obtained from 25 to 600 pg/mL (R²?>?0.99). The lower limit of detection was 8 pg/mL (S/N?>?3). The lower limit of quantification was 15 pg/mL (S/N?>?10; CV%?
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Evaluation of accurate mass and relative isotopic abundance measurements in the LTQ-orbitrap mass spectrometer for further metabolomics database building.
Anal. Chem.
PUBLISHED: 06-03-2010
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Recently, high-resolution mass spectrometry has been largely employed for compound identification, thanks to accurate mass measurements. As additional information, relative isotope abundance (RIA) is often needed to reduce the number of candidates prior to tandem MS(n). Here, we report on the evaluation of the LTQ-Orbitrap, in terms of accurate mass and RIA measurements for building further metabolomics spectral databases. Accurate mass measurements were achieved in the ppm range, using external calibration within 24 h, and remained at <5 ppm over a one-week period. The experimental relative abundances of (M+1) isotopic ions were evaluated in different data sets. First of all, 137 solutions of commercial compounds were analyzed by flow injection analysis in both the positive and negative ion modes. It was found that the ion abundance was the main factor impacting the accuracy of RIA measurements. It was possible to define some intensity thresholds above which errors were systematically <20% of their theoretical values. The same type of results were obtained with analyses from two biological media. Otherwise, no significant effect of ion transmission between the LTQ ion trap and the Orbitrap analyzer on RIA measurement errors was found, whereas the reliability of RIA measurements was dramatically improved by reducing the mass detection window. It was also observed that the signal integration method had a significant impact on RIA measurement errors, with the most-reliable results being obtained with peak height integrations. Finally, automatic integrations using the data preprocessing software XCMS and MZmine gave results similar to those obtained by manual integration, suggesting that it is relevant to use the RIA information in automatic elemental composition determination software from metabolomic peak tables.
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Ventilatory efficiency and the selection of patients for heart transplantation.
Circ Heart Fail
PUBLISHED: 02-22-2010
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Ventilatory efficiency, assessed by the slope of minute ventilation (VE) versus carbon dioxide production (VCO(2)), is a powerful prognostic marker in patients with chronic heart failure. We hypothesized that VE/VCO(2) slope would be more accurate than the current listing criteria for heart transplantation (HTx) in identifying patients likely to derive a survival benefit from this intervention.
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Distribution of left ventricular ejection fraction and heart rate values in a cohort of stable coronary patients: the INDYCE registry.
Arch Cardiovasc Dis
PUBLISHED: 02-17-2010
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The distribution of left ventricular ejection fraction (LVEF) - a key factor in coronary artery disease (CAD) patient management and prognostication - is poorly documented.
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Nonsteroidal anti-inflammatory drug treatment for postoperative pericardial effusion: a multicenter randomized, double-blind trial.
Ann. Intern. Med.
PUBLISHED: 02-04-2010
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The incidence of asymptomatic pericardial effusion is high after cardiac surgery. Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely prescribed in this setting, but no study has assessed their efficacy.
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Theoretical and experimental study of tropylium formation from substituted benzylpyridinium species.
J Mass Spectrom
PUBLISHED: 11-03-2009
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Fragmentation pathways of unsubstituted and substituted benzylpyridinium compounds were investigated using mass-analysed kinetic energy (MIKE) technique in combination with high level of quantum chemical calculations in the gas phase. Fast atom bombardment (FAB) source was used for ionisation of the studied compounds. The formation of both benzylium and tropylium species were investigated. Hybrid Hartree-Fock/Density Functional Theory calculations have been performed to assess the geometries and the energies of the transition states and intermediates. For each cases, different reaction pathways were investigated, and particularly in the case of the formation of tropylium species, the formation of the seven-membered ring before or after the loss of pyridine were studied. The effect of para-methyl and para-methoxy substituents on the activation energy of the rearrangement process to form thermodynamically stable tropylium compounds has been studied. Theoretical calculations showed competition between direct bond cleavage and rearrangement reactions to form benzylium and tropylium compounds, respectively. Experimental results also suggested that the rearrangement process takes place to yield stable tropylium under "soft ionisation techniques", such as FAB.
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Capacity of type I and II ligands to confer to estrogen receptor alpha an appropriate conformation for the recruitment of coactivators containing a LxxLL motif-Relationship with the regulation of receptor level and ERE-dependent transcription in MCF-7 cel
Biochem. Pharmacol.
PUBLISHED: 09-03-2009
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Estrogen receptor alpha (ERalpha) belongs to the superfamily of nuclear receptors and as such acts as a ligand-modulated transcription factor. Ligands elicit in ERalpha conformational changes leading to the recruitment of coactivators required for the transactivation of target genes via cognate response elements. In many cells, activated ERalpha also undergoes downregulation by proteolysis mediated by the ubiquitin/proteasome system. Although these various molecular processes have been well characterized, little is known as to which extent they are interrelated. In the present study, we used a panel of type I (estradiol derivatives and "linear", non-steroidal ligands) and type II ("angular" ligands) estrogens, in order to identify possible relationships between ligand binding affinity, recruitment of LxxLL-containing coactivators, ERalpha downregulation in MCF-7 cells and related transactivation activity of ligand-bound ERalpha. For type I estrogens, there was a clear-cut relationship between ligand binding affinity, hydrophobicity around C-11 of estradiol and ability of ERalpha to associate with LxxLL motifs, both in cell-free condition and in vivo (MCF-7 cells). Moreover, LxxLL motif recruitment by ERalpha seemed to be a prerequisite for the downregulation of the receptor. By contrast, type II ligands, as well as estradiol derivatives bearing a bulky side chain at 11beta, had much less tendency to promote ERalpha-LxxLL interaction or even behaved as antagonists in this respect, in agreement with the well known partial estrogenicity/antiestrogenicity of some of these compounds. Interestingly, some type II ligands which antagonized LxxLL motif recruitment were nonetheless able to enhance ERalpha-mediated gene transactivation.
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Hyphenation of atmospheric pressure chemical ionisation mass spectrometry to supercritical fluid chromatography for polar car lubricant additives analysis.
J Chromatogr A
PUBLISHED: 07-25-2009
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Car lubricant additives are added to mineral or synthetic base stocks to improve viscosity and resistance to oxidation of the lubricant and to limit wear of engines. As they belong to various chemical classes and are added to a very complex medium, the base stock, their detailed chromatographic analysis is very difficult and time consuming. In a previous paper, it was demonstrated that supercritical fluid chromatography (SFC) allows the elution of common low-molecular-weight additives. Since their total resolution could not be achieved owing to the limited peak capacity of packed columns, the hyphenation of selective and informative detection methods such as atomic emission detection (AED) was required. Further to results obtained in SFC-AED, this work describes the hyphenation of SFC to atmospheric pressure chemical ionisation ion trap mass spectrometry (MS). SFC-MS hyphenation is detailed: temperature, flow rates of gas and mobile phase introduced in the source, position of the restrictor, ionisation additives and conditions of autotune are studied. Car lubricant monitoring requires negative and positive ionisation modes with or without the addition of ionisation auxiliary solvent according to the nature of additives. Moreover, when sensitivity is of major concern for a selected additive, the autotuning routine of the MS has to be performed in conditions as close as possible to analytical conditions, i.e. under subcritical conditions. Unambiguous identification and structure elucidation of several additives in formulated car lubricants are also presented.
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Stereochemical effects during [M-H]- dissociations of epimeric 11-OH-17beta-estradiols and distant electronic effects of substituents at C(11) position on gas phase acidity.
J. Am. Soc. Mass Spectrom.
PUBLISHED: 06-19-2009
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The affinity of estradiol derivatives for the estrogen receptor (ER) depends strongly on nature and stereochemistry of substituents in C(11) position of the 17beta-estradiol (I). In this work, the stereochemistry effects of the 11alpha-OH-17beta-estradiol (III(alpha)) and 11beta-OH-17beta-estradiol (III(beta)) were investigated using CID experiments and gas-phase acidity (DeltaH degrees (acid)) determination. The CID experiments showed that the steroids decompose via different pathways involving competitive dissociations with rate constants depending upon the alpha/beta C(11) stereochemistry. It was shown that the fragmentations of both deprotonated [III(alpha)-H]- and [III(beta)-H]- epimers were initiated by the deprotonation of the most acidic site, i.e. the phenolic hydroxyl at C(3). This view was confirmed by H/D exchange and double resonance experiments. Furthermore, the DeltaH degrees (acid) of both epimers (III(alpha) and III(beta)), 17beta-estradiol (I), and 17-desoxyestradiol (II) was determined using the extended Cooks kinetic method. The resulting values allowed us to classify steroids as a function of their gas-phase acidity as follows: (III(beta)) > (II) > (I) > (III(alpha)). Interestingly, the alpha/beta C(11) stereochemistry appeared to influence strongly the gas-phase acidity. This phenomenon could be explained through stereospecific proton interaction with pi-orbital cloud of A ring, which was confirmed by theoretical calculation.
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Benefits of exercise training in chronic heart failure.
Arch Cardiovasc Dis
PUBLISHED: 03-25-2009
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Exercise training performed in cardiac rehabilitation centres is an adjuvant therapy in chronic heart failure patients with left ventricular dysfunction; it decreases the deleterious consequences of chronic heart failure. Exercise training attenuates neurohormonal stimulation, the production of proinflammatory cytokines and natriuretic peptide overexpression. Trained patients showed a significant decrease in the peripheral organ injuries encountered in chronic heart failure, with a reduction in vascular resistance and improvements in endothelial dysfunction and the oxidative capacity of peripheral muscles, without a deleterious effect on left ventricular remodelling. Ultimately, exercise training leads to a notable improvement in ventilatory capacity. These beneficial effects are accompanied by improvements in symptoms at rest, exercise capacity and quality of life. Several training programmes are in current use: exercise training sessions always include endurance exercise performed either at a constant load intensity or with interval training, combining periods of exercise performed at high intensity with periods performed at low intensity. Most of the time, training programmes also include resistance training sessions, which improves large muscle strength. Exercise training programmes seem to have a favourable effect on prognosis, even if the results of Heart Failure: a Controlled Trial Investigating Outcomes of Exercise Training (HF-ACTION) remain controversial, emphasizing the difficulty in monitoring observance and the importance of compliance with a long-term exercise training programme. Patients who do not improve their exercise capacity significantly after an exercise training programme have a poorer prognosis.
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Gold- and platinum-catalyzed cycloisomerization of enynyl esters versus allenenyl esters: an experimental and theoretical study.
Chemistry
PUBLISHED: 02-10-2009
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Ester-way to heaven: Unexpected formation of bicyclo[3.1.0]hexene 4 was the main focus of combined experimental and theoretical studies on the Au-catalyzed cycloisomerization of branched dienyne 1 (see scheme), which provided better understanding of the mechanistic details governing the cyclization of enynes bearing a propargylic ester group.Experimental and theoretical studies on Au- and Pt-catalyzed cycloisomerization of a branched dienyne with an acetate group at the propargylic position are presented. The peculiar architecture of the dienyne precursor, which has both a 1,6- and a 1,5-enyne skeleton, leads, in the presence of alkynophilic gold catalysts, to mixtures of bicyclic compounds 3, 4, and 5. Formation of unprecedented bicyclo[3.1.0]hexene 5 is the main focus of this study. The effect of the ancillary ligand on the gold center was examined and found to be crucial for formation of 5. Further mechanistic studies, involving cyclization of an enantioenriched dienyne precursor, (18)O-labeling experiments, and DFT calculations, allowed an unprecedented reaction pathway to be proposed. We show that bicyclo[3.1.0]hexene 5 is likely formed by a 1,3-OAc shift/allene-ene cyclization/1,2-OAc shift sequence, as calculated by DFT and supported by Au-catalyzed cyclization of isolated allenenyl acetate 7, which leads to improved selectivity in the formation of 5. Additionally, the possibility of OAc migration from allenyl acetates was supported by a trapping experiment with styrene that afforded the corresponding cyclopropane derivative. This unprecedented generation of a vinyl metal carbene from an allenyl ester supports a facile enynyl ester/allenenyl ester equilibrium. Further examination of the difference in reactivity between enynyl acetates and their corresponding [3,3]-rearranged allenenyl acetates toward Au- and Pt-catalyzed cycloisomerization is also presented.
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Urine ratio of tetrahydrocortisol to tetrahydrodeoxycortisol to screen for the systemic administration of cortisone and hydrocortisone.
Forensic Sci. Int.
PUBLISHED: 01-29-2009
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We use gas chromatography-mass spectrometry (GC-MS) to determine the urine peak area ratio of tetrahydrocortisol (THF) to tetrahydrodeoxycortisol (THS) in spot urine samples of eight male volunteers after a single intramuscular injection of 100 mg hydrocortisone (HC) and after a single oral administration of 10 mg HC at six different post-treatment times over 24 h with 1 week between the two treatments. Control spot urine samples were also obtained from a group of 100 volunteers of each sex for GC-MS analysis. In addition, one female volunteer was collected for GC-MS and isotope ratio mass spectrometry (IRMS) analysis after a single oral administration of 40 mg HC and 40 mg cortisone (C) at 15 and 10 different post-treatment times over 30 h, respectively. IRMS analysis focused on the acetylated derivative of 11-keto-etiocholanolone (11KE) and 11beta-hydroxy-etiocholanolone (11OHE) as target metabolites, and on androsterone (A) as an endogenous reference compound (ERC) for calculating the corresponding delta(13)C (per thousand) depletion values. There was a small but significant sex-related difference for the THF/THS ratio in the control group with mean THF/THS ratio values of 10 and 13.5 for women and men, respectively. A cut-off value of 28 (mean+2 S.D.) for the THF/THS ratio offered a narrow detection window with 39% of suspicious samples after HC-oral treatment, and a wide detection window with 94% of suspicious samples after HC-intramuscular administration in men. For the woman the same cut-off value offered a wide detection window after HC and C administration with 100% and 90% of suspicious samples, respectively. On the basis of a cut-off value of 3 per thousand for the delta(13)C (per thousand) depletion, the exogenous origin was widely evidenced for at least one target compound in 93% and 80% of the HC and C samples, respectively. We conclude by discussing the predictive ability of the urine THF/THS ratio and its usefulness in pointing out suspicious samples resulting from the systemic administration of HC and C.
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Organ preservation with concurrent chemoradiation for advanced laryngeal cancer: are we succeeding?
Int. J. Radiat. Oncol. Biol. Phys.
PUBLISHED: 01-28-2009
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To determine the rates of organ preservation and function in patients with advanced laryngeal and hypopharyngeal carcinomas treated with concurrent chemoradiotherapy (CRT).
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Outcome with neck dissection after chemoradiation for N3 head-and-neck squamous cell carcinoma.
Int. J. Radiat. Oncol. Biol. Phys.
PUBLISHED: 01-24-2009
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To evaluate the role of neck dissection (ND) after chemoradiation therapy (CRT) for head and neck squamous cell carcinoma (HNSCC) with N3 disease.
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Concurrent chemoradiation with carboplatin-5-fluorouracil versus cisplatin in locally advanced oropharyngeal cancers: is more always better?
Int. J. Radiat. Oncol. Biol. Phys.
PUBLISHED: 01-12-2009
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The optimal chemotherapy regimen remains undefined in the treatment of locally advanced oropharyngeal cancer by concomitant chemoradiation. This article compares two platinum-based chemotherapy regimens.
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In Vitro Antioxidant Activity of Two 6-(propan-2-yl)-4-methyl-morpholine-2,5-diones.
Acta Chim Slov
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In vitro antioxidant activity of two cyclodidepsipeptides, 3-(2-methylpropyl)-6-(propan-2-yl)-4-methyl-morpholine-2,5-dione and 3,6-di(propan-2-yl)-4-methyl-morpholine-2,5-dione, was investigated. Our data indicate moderate antioxidant potentials of the two studied cyclodepsipeptides. A high correlation between 2,2-diphenyl-1-picrylhydrazyl (DPPH)-radical scavenging capacity and total reducing power were found. According to the density functional theory (DFT) calculations, the most probable mechanism of antioxidant action is hydrogen atom abstraction from the activated C-H group at 3-position in the morpholinedione ring. To the best of our knowledge this is the first report about the antioxidant properties of morpholine-2,5-diones derivatives.
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Prompt and slow electron-detachment-dissociation/electron-photodetachment-dissociation of a 21-mer peptide.
Chemistry
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Electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) are relatively new dissociation methods that involve electron detachment followed by radical-driven dissociation from multiply deprotonated species. EDD yields prompt dissociation whereas only electron detachment is obtained by EPD; subsequent vibrational activation of the charge-reduced radical anion is required to obtain the product ions. Herein, the fragmentation patterns that were obtained by EDD and by vibrational activation of the charge-reduced radical anions that were produced through EDD or EPD (activated-EDD and activated-EPD) were compared. The observed differences were related to the dissociation kinetics and/or the contribution of electron-induced dissociation (EID). Time-resolved double-resonance experiments were performed to measure the dissociation rate constants of the EDD product ions. Differences in the formation kinetics were revealed between the classical EDD/EPD a(?)(i)/x(j) complementary ions and some a(?)(i)/c(i)/z(?)(j) product ions, which were produced with slower dissociation rate constants, owing to the presence of specific neighbouring side chains. A new fragmentation pathway is proposed for the formation of the slow-kinetics a(?)(i) ions.
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Distinctive gas-phase fragmentation pathway of the mitorubramines, novel secondary metabolites from Hypoxylon fragiforme.
Rapid Commun. Mass Spectrom.
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Azaphilones, belonging to the class of mitorubrins usually produced in Hypoxylon fragiforme, react easily with amino groups, giving amine derivatives, mitorubramines. These secondary metabolites exhibit a wide range of biological activities. Finding new secondary metabolites from fungi is important, and electrospray ionization (ESI) high-resolution mass spectrometry (HRMS) coupled with sequential MS(n) experiments has become a method of choice for the chemotaxonomic classification of fungi.
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Electronic effects of 11? substituted 17?-estradiol derivatives and instrumental effects on the relative gas phase acidity.
J. Am. Soc. Mass Spectrom.
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Numerous studies have highlighted the role of the proton donor characteristics of the phenol group of 17?-estradiol (E(2)) in its association with the estrogen receptor alpha (ER?). Since the substitutions at position C((11)) have been reported to modulate this association, we hypothesized that such substitutions may modify the phenol acidity. Hence, phenol gas-phase acidity of nine C((11))-substituted E(2)-derivatives were evaluated using the extended Cooks kinetic method, which is a method widely used to determine thermochemical properties by mass spectrometry. To enhance accuracy in data collection we recorded data from several instruments, including quadrupole ion trap, triple quadrupole, and hybrid QqTOF. Indeed, we report for the first time the use of the QqTOF instrument to provide a novel means to improve data accuracy by giving access to an intermediate effective temperature range. All experimental gas-phase acidity values were supported by theoretical calculations. Our results confirmed the ability of distant substituents at C((11)) to modulate the phenol acidity through electrostatic interactions, electron withdrawing inductive effects, and mesomeric effects. However, no relationship was found between the phenol gas-phase acidity of investigated steroids and their binding affinity for ER? assessed in solution. Thus, our results highlight that the intrinsic properties of the hormone do not influence sufficiently the stabilization of the hormone/ER? complex. It is more likely that such stabilization would be more related to factors depending on the environment within the binding pocket such as hydrophobic, steric as well as direct intermolecular electrostatic effects between ER? residues and the substituted steroidal estrogens.
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High-resolution mass spectrometry and hydrogen/deuterium exchange study of mitorubrin azaphilones and nitrogenized analogues.
J Mass Spectrom
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Azaphilones represent numerous groups of wild fungal secondary metabolites that exhibit exceptional tendency to bind to nitrogen atoms in various molecules, especially those containing the amine group. Nitrogenized analogues of mitorubrin azaphilones, natural secondary metabolites of Hypoxylon fragiforme fungus, have been detected in the fungal methanol extract in very low concentrations. Positive electrospray ionization interfaced with high-resolution mass spectrometry was applied for confirmation of the elemental composition of protonated species. Collision-induced dissociation (CID) experiments have been performed, and fragmentation mechanisms have been proposed. Additional information regarding both secondary metabolite analogue families has been reached by application of gas-phase proton/deuterium (H/D) exchanges performed in the collision cell of a triple quadrupole mass spectrometer. An incomplete H/D exchange with one proton less than expected was observed for both protonated mitorubrin azaphilones and their nitrogenized analogues. By means of the density functional theory, an appropriate explanation of this behavior was provided, and it revealed some information concerning gas-phase H/D exchange mechanism and protonation sites.
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Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer.
Anal. Chem.
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Metabolic profiles of biofluids obtained by atmospheric pressure ionization mass spectrometry-based technologies contain hundreds to thousands of features, most of them remaining unknown or at least not characterized in analytical systems. We report here on the annotation of the human adult urinary metabolome and metabolite identification from electrospray ionization mass spectrometry (ESI-MS)-based metabolomics data sets. Features of biological interest were first of all annotated using the ESI-MS database of the laboratory. They were also grouped, thanks to software tools, and annotated using public databases. Metabolite identification was achieved using two complementary approaches: (i) formal identification by matching chromatographic retention times, mass spectra, and also product ion spectra (if required) of metabolites to be characterized in biological data sets to those of reference compounds and (ii) putative identification from biological data thanks to MS/MS experiments for metabolites not available in our chemical library. By these means, 384 metabolites corresponding to 1484 annotated features (659 in negative ion mode and 825 in positive ion mode) were characterized in human urine samples. Of these metabolites, 192 and 66 were formally and putatively identified, respectively, and 54 are reported in human urine for the first time. These lists of features could be used by other laboratories to annotate their ESI-MS metabolomics data sets.
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Formation and characterization of gaseous adducts of carbon dioxide to magnesium, (CO2)MgX- (X=OH, Cl, Br).
Angew. Chem. Int. Ed. Engl.
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A good fix: the structure and chemical reactivity of a reduced form of CO(2) bonded to magnesium, XMg(?(2)-O(2)C)(-), is reported. Upon reaction with water it loses CO, while it adds CH(3) upon reaction with alkyl halides, thereby signifying nucleophilicity of the carbon atom in XMg(?(2)-O(2)C)(-) in S(N)2 reactions.
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Determination of peptide topology through time-resolved double-resonance under electron capture dissociation conditions.
Anal. Chem.
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Characterizing the conformation of biomolecules by mass spectrometry still represents a challenge. With their knotted structure involving a N-terminal macrolactam ring where the C-terminal tail of the peptide is threaded and sterically trapped, lasso peptides constitute an attractive model for developing methods for characterizing gas-phase conformation, through comparison with their unknotted topoisomers. Here, the kinetics of electron capture dissociation (ECD) of a lasso peptide, capistruin, was investigated by electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry and compared to that of its branched-cyclic topoisomer, lactam-capistruin. Both peptides produced rather similar ECD spectra but showed different extent of H(•) transfer from c(i) to z(j)(•) ions. Time-resolved double-resonance experiments under ECD conditions were performed to measure the formation rate constants of typical product ions. Such experiments showed that certain product ions, in particular those related to H(•) transfer, proceeded through long-lived complexes for capistruin, while fast dissociation processes predominated for lactam-capistruin. The formation rate constants of specific ECD product ions enabled a clear differentiation of the lasso and branched-cyclic topoisomers. These results indicate that the formation kinetics of ECD product ions constitute a new way to explore the conformation of biomolecules and distinguish between topoisomers and, more generally, conformers.
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Rapid quantification of clostridial epsilon toxin in complex food and biological matrixes by immunopurification and ultraperformance liquid chromatography-tandem mass spectrometry.
Anal. Chem.
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Epsilon toxin (ETX) is one of the most lethal toxins produced by Clostridium species and is considered as a potential bioterrorist weapon. Here, we present a rapid mass spectrometry-based method for ETX quantification in complex matrixes. As a prerequisite, naturally occurring prototoxin and toxin species were first structurally characterized by top-down and bottom-up experiments, to identify the most pertinent peptides for quantification. Following selective ETX immunoextraction and trypsin digestion, two proteotypic peptides shared by all the toxin forms were separated by ultraperformance liquid chromatography (UPLC) and monitored by ESI-MS (electrospray ionization-mass spectrometry) operating in the multiple reaction monitoring mode (MRM) with collision-induced dissociation. Thorough protocol optimization, i.e., a 15 min immunocapture, a 2 h enzymatic digestion, and an UPLC-MS/MS detection, allowed the whole quantification process including the calibration curve to be performed in less than 4 h, without compromising assay robustness and sensitivity. The assay sensitivity in milk and serum was estimated at 5 ng·mL(-1) for ETX, making this approach complementary to enzyme linked immunosorbent assay (ELISA) techniques.
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Gas-phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation, structures and electron capture dissociation.
J Mass Spectrom
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Copper complexes with a cyclic D-His-?-Ala-L-His-L-Lys and all-L-His-?-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06-2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side-chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c-HAHK + H)](2+) and [Cu(c-HAHK - H)](2+) type with closed electronic shells followed similar orders when treated by the B3LYP and M06-2X functionals. Large differences between relative energies calculated by these methods were obtained for open-shell complexes of the [Cu(c-HAHK)](2+) type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c-HAHK - H)](2+) complexes, solution H/D exchange involved only the N-H protons, resulting in the exchange of up to seven protons, as established by ultra-high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas-phase ions that were deprotonated at the peptide C(?) positions.
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Biophysical studies of the interaction between calmodulin and the R²??-T³¹¹ region of human estrogen receptor ? reveals an atypical binding process.
Biochem. Biophys. Res. Commun.
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The transcriptional activity of human estrogen receptor ER? is modulated by a number of coregulatory proteins among which calmodulin (CaM). Segment 295-311 in the hinge region of ER? has previously been proposed to be the CaM binding site. In this work, we investigate the molecular mechanism of the interaction of CaM with peptides derived from the hinge region of ER?, using a biophysical approach combining isothermal titration calorimetry, fluorescence, CD and NMR. The ER?17p peptide, corresponding to the previously identified 295-311 region of ER?, recruits mainly the C-terminal domain of Ca(4)CaM, as shown by NMR spectroscopy. In contrast, a longer peptide, ER?25p, extended on the N-terminal side (residues 287-311) interacts with both N- and C-terminal domains of Ca(4)CaM. These results lead to a new delineation of the CaM binding site, encompassing residues 287-294. In particular, fluorescence spectroscopy reveals that the conserved W(292) residue is engaged within hydrophobic pockets on Ca(4)CaM. ITC results show that ER?25p binds Ca(4)CaM with an atypical 2:1 stoichiometry and a dissociation constant in the micromolar range. Based on the NMR titration of Ca(4)CaM by ER?25p showing a biphasic behavior for several residues, we suggest that concerted conformational changes of CaM domains may be required to accommodate the binding of a second peptide. CD spectra indicate that ER?25p partially folds into an ?-helix upon binding to Ca(4)CaM. Hence, ER?25p is a new CaM-binding ligand that could be appropriate for the synthesis of derivatives able to control ER-dependent transcription, particularly in the context of hormone-dependent breast tumors.
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